{"doi":"10.1242/dev.200356","title":"Normal Table of <i>Xenopus</i> development: a new graphical resource","abstract":"Normal tables of development are essential for studies of embryogenesis, serving as an important resource for model organisms, including the frog Xenopus laevis. Xenopus has long been used to study developmental and cell biology, and is an increasingly important model for human birth defects and disease, genomics, proteomics and toxicology. Scientists utilize Nieuwkoop and Faber's classic 'Normal Table of Xenopus laevis (Daudin)' and accompanying illustrations to enable experimental reproducibility and reuse the illustrations in new publications and teaching. However, it is no longer possible to obtain permission for these copyrighted illustrations. We present 133 new, high-quality illustrations of X. laevis development from fertilization to metamorphosis, with additional views that were not available in the original collection. All the images are available on Xenbase, the Xenopus knowledgebase (http://www.xenbase.org/entry/zahn.do), for download and reuse under an attributable, non-commercial creative commons license. Additionally, we have compiled a 'Landmarks Table' of key morphological features and marker gene expression that can be used to distinguish stages quickly and reliably (https://www.xenbase.org/entry/landmarks-table.do). This new open-access resource will facilitate Xenopus research and teaching in the decades to come.","journal":"Development","year":2022,"id":232978,"datarank":2.8985229387509377,"base_score":5.030437921392435,"endowment":5.030437921392435,"self_citation_contribution":0.7545656882088654,"citation_network_contribution":2.1439572505420723,"self_endowment_contribution":0.7545656882088654,"citer_contribution":2.1439572505420723,"corpus_percentile":92.43443954513808,"corpus_rank":979,"citation_count":152,"citer_count":100,"citers_with_citation_signal":98,"citers_with_endowment":98,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.7705,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":50.0,"fair_percentile":62.702537450321,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":844488,"name":"Christina James‐Zorn","orcid":"0000-0001-5495-4588","position":1,"is_corresponding":false},{"id":844489,"name":"Virgilio Ponferrada","orcid":"0000-0002-8590-7183","position":2,"is_corresponding":false},{"id":844490,"name":"Dany Spencer Adams","orcid":"0000-0003-2024-9746","position":3,"is_corresponding":false},{"id":844491,"name":"Julia Grzymkowski","orcid":"0000-0002-8465-0056","position":4,"is_corresponding":false},{"id":844492,"name":"Daniel R. Buchholz","orcid":"0000-0002-9881-9924","position":5,"is_corresponding":false},{"id":799220,"name":"Nanette M. Nascone‐Yoder","orcid":"0000-0003-1301-5298","position":6,"is_corresponding":false},{"id":332033,"name":"Marko E. Horb","orcid":"0000-0002-5067-0518","position":7,"is_corresponding":false},{"id":380771,"name":"Sally A. Moody","orcid":"0000-0003-4192-1087","position":8,"is_corresponding":false},{"id":822218,"name":"Peter D. Vize","orcid":"0000-0001-8026-0424","position":9,"is_corresponding":false},{"id":247690,"name":"Aaron M. Zorn","orcid":"0000-0003-3217-3590","position":10,"is_corresponding":false},{"id":844487,"name":"Natalya Zahn","orcid":"0000-0002-9982-3909","position":0,"is_corresponding":true}],"reference_count":90,"raw_metadata":null,"created_at":"2026-07-19T00:21:18.683916Z","pmid":"35833709","pmcid":"PMC9445888","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":50.0,"fair_a":50.0,"fair_i":100.0,"fair_r":41.6667,"fair_zscore":0.6155,"fair_rationale":{"fair_score":50.0,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All the images are available on Xenbase, the Xenopus knowledgebase ( http://www.xenbase.org/entry/zahn.do )","grounded":true,"rationale":"The dataset is given a web URL, not a persistent identifier scheme (DOI, Handle, etc.).","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"Xenbase","grounded":false,"rationale":"Xenbase is named as the repository holding the data. [downgraded to 'partial' — no verifiable quote from the paper] [majority verdict 'partial' (3/5 passes agreed)]","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All the Zahn drawings (those presented here and the earlier XenHead set) are available on Xenbase (http://www.xenbase.org/entry/zahn.do) through an attributable, non-commercial creative commons license (CC BY-NC 4.0).","grounded":false,"rationale":"The statement points to a repository record (Xenbase) with a URL and license. 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[majority verdict 'partial' (4/5 passes agreed)]","anchors":["RDA-F2-01M — 'Rich metadata is provided to allow discovery' (priority Essential)","FsF-F2-01M — F-UJI: 'Metadata includes descriptive core elements to support data findability'","FsF-R1-01MD — F-UJI: 'Metadata specifies the content of the data'"],"scored":false,"signal":null},{"key":"f_dataset_cited","label":"Dataset formally cited","kind":"llm","weight":1.0,"fraction":0.5,"verdict":"partial","evidence":"All the images are available on Xenbase, the Xenopus knowledgebase ( http://www.xenbase.org/entry/zahn.do )","grounded":true,"rationale":"The dataset identifier (URL) appears only in the body text, not in the reference list. [majority verdict 'partial' (3/5 passes agreed)]","anchors":["FORCE11 Joint Declaration of Data Citation Principles (2014) — data should be cited as a first-","RDA-F3-01M — metadata clearly and explicitly includes the identifier of the data it describes","FsF-F3-01M — F-UJI: 'Metadata includes the identifier of the data it describes'"],"scored":true,"signal":null}]},"A":{"name":"Accessible","score":50.0,"criteria":[{"key":"a_data_openly_accessible","label":"Access route free of preconditions","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"All the Zahn drawings (those presented here and the earlier XenHead set) are available on Xenbase (http://www.xenbase.org/entry/zahn.do) through an attributable, non-commercial creative commons license (CC BY-NC 4.0).","grounded":false,"rationale":"The data are accessible without precondition; the license only restricts reuse, not access. 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[majority verdict 'yes' (3/5 passes agreed)]","anchors":["FsF-A1-01M — F-UJI: 'Metadata contains access level and access conditions of the data'","RDA-A1-01M — metadata contains information to enable the user to get access to the data","COAR Controlled Vocabularies — Access Rights v1.0 (open / embargoed / restricted / metadata-onl"],"scored":false,"signal":null},{"key":"a_controlled_access_for_sensitive","label":"Gatekeeper for sensitive data","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The data are not sensitive or human-subject, so no gatekeeper is named.","anchors":["NIH Genomic Data Sharing Policy (NOT-OD-14-124) — controlled-access via a Data Access Committee","RDA-A1.2-01D — 'Data is accessible through an access protocol that supports authentication and ","NIH DMS Policy Element 5 (NOT-OD-21-014) — Access, Distribution, or Reuse Considerations (conse"],"scored":false,"signal":null},{"key":"a_timeline_retention","label":"Availability timing & retention","kind":"llm","weight":0.5,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No persistence commitment or availability timing is stated for the data. [majority verdict 'no' (4/5 passes agreed)]","anchors":["NIH DMS Plan Element 4 (NOT-OD-21-014) — Data Preservation, Access, and Associated Timelines","NSTC Desirable Characteristics (2022), Organizational Infrastructure: 'Retention Policy'","RDA-A2-01M — 'Metadata is guaranteed to remain available after data is no longer available'"],"scored":false,"signal":null}]},"I":{"name":"Interoperable","score":100.0,"criteria":[{"key":"i_open_nonproprietary_format","label":"Open file format","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"The Zahn drawings presented here and those from the XenHead project ( Zahn et al., 2017 ) are available as individual digital files (jpg format) and as a compiled printable sheet (pdf format) on Xenbase","grounded":true,"rationale":"JPEG and PDF are open, non-proprietary file formats. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["FsF-R1.3-02D — F-UJI: 'Data is available in a file format recommended by the target research co","RDA-R1.3-02D — data is expressed in a machine-understandable community standard","RDA-I1-01D — data uses a knowledge representation expressed in a standardised format"],"scored":true,"signal":null},{"key":"i_community_standard_vocabulary","label":"Community standard / vocabulary","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"In Xenbase, developmental stages, cell types, tissues and organs are represented in the Xenopus Anatomical Ontology (the XAO), with term definitions being directly adapted from the Normal Table","grounded":true,"rationale":"The XAO is a community standard metadata ontology. [majority verdict 'yes' (3/5 passes agreed)]","anchors":["RDA-R1.3-01M — 'Metadata complies with a community standard' (priority Essential)","RDA-R1.3-01D — 'Data complies with a community standard'","RDA-I2-01M — '(Meta)data use vocabularies that follow FAIR principles'"],"scored":false,"signal":null},{"key":"i_qualified_references","label":"Identifiers for the resources the data depend on","kind":"llm","weight":0.5,"fraction":1.0,"verdict":"yes","evidence":"RRID:SCR_013731","grounded":true,"rationale":"The paper provides an RRID for the National Xenopus Resource, an identifier for a resource other than the dataset. [majority verdict 'yes' (4/5 passes agreed)]","anchors":["RDA-I3-01M — '(meta)data include references to other (meta)data'","RDA-I3-03M — 'metadata includes qualified references to other metadata'","FsF-I3-01M — F-UJI: 'Metadata includes links between the data and its related entities'"],"scored":false,"signal":null}]},"R":{"name":"Reusable","score":41.67,"criteria":[{"key":"r_reuse_license","label":"Reuse licence","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"through an attributable, non-commercial creative commons license (CC BY-NC 4.0)","grounded":true,"rationale":"The license is CC BY-NC 4.0, which is not on the open list (CC0, CC BY, etc.).","anchors":["RDA-R1.1-01M — 'Metadata includes information about the licence under which the data can be reu","RDA-R1.1-02M — 'Metadata refers to a standard reuse licence'","RDA-R1.1-03M — 'Metadata refers to a machine-understandable reuse licence'"],"scored":true,"signal":null},{"key":"r_provenance_methods","label":"Provenance of the data","kind":"llm","weight":1.0,"fraction":1.0,"verdict":"yes","evidence":"Specimens were photographed using a Zeiss steREO Discovery.V12 microscope with an AxioCam MRc camera","grounded":true,"rationale":"The text names specific instruments used to produce the data.","anchors":["RDA-R1.2-01M — 'Metadata includes provenance information according to community- specific standa","FsF-R1.2-01M — F-UJI: 'Metadata includes provenance information about data creation or generati","W3C PROV-O (W3C Recommendation, 2013) — the entity/activity/agent model of provenance"],"scored":false,"signal":null},{"key":"r_documentation_codebook","label":"Documentation / codebook","kind":"llm","weight":1.0,"fraction":0.0,"verdict":"no","evidence":"Table S1","grounded":false,"rationale":"The Landmarks Table (Table S1) defines staging landmarks inside the article, not as a separate file shipped with the data. 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[majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For proteomics data, deposit in PRIDE (PXD accession) or ProteomeXchange.","Remove the precondition or justify it. 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